Re: [Treebase-devel] Deploying under Tomcat

[youjun g. <you...@ya...>]

Vladimir,

Why do you want to deploy a new TreeBASE installation? If you just want to
add a java encrypt implementation like MD5 to TreeBASE code, I my be able to
help with it. Then you can focus on some other task.

Youjun

On Tue, Dec 15, 2009 at 5:50 PM, Vladimir Gapeyev <vga...@ne...>wrote:

>
> On Dec 15, 2009, at 4:41 PM, youjun guo wrote:
>
>  Vladimir,
>>
>> jdbc.properties should be add to main/resource of treebase-core before
>> bilud, and it will be built into treebase-core jar file.
>>
>>
> Thanks, this has moved me forward.  The deployment still fails, apparently
> due to mesquite again. See the excerpt from logs/catalina.out below.
>
> I do see numerous Eclipse complaints about failing 'import
> mesquite.lib.*'., which I did not see earlier in the day!  I did update from
> SVN, as well as all Maven-related update commands I could see in the UI.
>
> --Vladimir
>
>
>
> [main] ERROR org.springframework.web.context.ContextLoader - Context
> initialization failed
> org.springframework.beans.factory.BeanCreationException: Error creating
> bean with name 'sessionFactory' defined in URL
> [jar:file:/Users/vgapeyev/Work/TreeBase/devel/applications/apache-tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar!/applicationContext-dao.xml]:
> Invocation of init method failed; nested exception is
> org.hibernate.InstantiationException: could not instantiate test
> objectorg.cipres.treebase.domain.taxon.TaxonLabelSet
> Caused by:
> org.hibernate.InstantiationException: could not instantiate test
> objectorg.cipres.treebase.domain.taxon.TaxonLabelSet
>        at
> org.hibernate.engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:25)
>        at
> org.hibernate.engine.UnsavedValueFactory.getUnsavedIdentifierValue(UnsavedValueFactory.java:44)
>        at
> org.hibernate.tuple.PropertyFactory.buildIdentifierProperty(PropertyFactory.java:44)
>        at
> org.hibernate.tuple.entity.EntityMetamodel.<init>(EntityMetamodel.java:124)
>        at
> org.hibernate.persister.entity.AbstractEntityPersister.<init>(AbstractEntityPersister.java:434)
>        at
> org.hibernate.persister.entity.SingleTableEntityPersister.<init>(SingleTableEntityPersister.java:109)
>        at
> org.hibernate.persister.PersisterFactory.createClassPersister(PersisterFactory.java:55)
>        at
> org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:226)
>        at
> org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1300)
>        at
> org.hibernate.cfg.AnnotationConfiguration.buildSessionFactory(AnnotationConfiguration.java:859)
>        at
> org.springframework.orm.hibernate3.LocalSessionFactoryBean.newSessionFactory(LocalSessionFactoryBean.java:805)
>        at
> org.springframework.orm.hibernate3.LocalSessionFactoryBean.buildSessionFactory(LocalSessionFactoryBean.java:745)
>        at
> org.springframework.orm.hibernate3.AbstractSessionFactoryBean.afterPropertiesSet(AbstractSessionFactoryBean.java:134)
>        at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1198)
>        at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
>        at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:427)
>        at
> org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:249)
>        at
> org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:155)
>        at
> org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:246)
>        at
> org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160)
>        at
> org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:285)
>        at
> org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:352)
>        at
> org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:245)
>        at
> org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:188)
>        at
> org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:49)
>        at
> org.cipres.treebase.web.listeners.StartupListener.contextInitialized(StartupListener.java:45)
>        at
> org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3795)
>        at
> org.apache.catalina.core.StandardContext.start(StandardContext.java:4252)
>        at
> org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
>        at
> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740)
>        at
> org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544)
>        at
> org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:831)
>        at
> org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720)
>        at
> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490)
>        at
> org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
>        at
> org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311)
>        at
> org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
>        at
> org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022)
>        at
> org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
>        at
> org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014)
>        at
> org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
>        at
> org.apache.catalina.core.StandardService.start(StandardService.java:448)
>        at
> org.apache.catalina.core.StandardServer.start(StandardServer.java:700)
>        at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>        at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
>        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
> Caused by: java.lang.reflect.InvocationTargetException
>        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
>        at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
>        at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
>        at java.lang.reflect.Constructor.newInstance(Constructor.java:501)
>        at
> org.hibernate.engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:22)
>        ... 49 more
> Caused by: java.lang.Error: Unresolved compilation problems:
>        The import mesquite.lib cannot be resolved
>        StringUtil cannot be resolved
>        StringUtil cannot be resolved
>        StringUtil cannot be resolved
>        StringUtil cannot be resolved
>
>        at
> org.cipres.treebase.domain.taxon.TaxonLabelSet.<init>(TaxonLabelSet.java:18)
>        ... 54 more
>
>
>
>
>
>